GapMind for catabolism of small carbon sources

 

propionate catabolism in Dechlorosoma suillum PS

Best path

mctC, prpE, pccA, pccB, epi, mcm-large, mcm-small

Also see fitness data for the top candidates

Rules

Overview: Propionate degradation in GapMind is based on MetaCyc pathways for the 2-methylcitrate cycle (link, link) and for propanoyl-CoA degradation (link, link).

24 steps (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mctC propionate:H+ symporter Dsui_0290 Dsui_0522
prpE propionyl-CoA synthetase Dsui_2925 Dsui_2003
pccA propionyl-CoA carboxylase, alpha subunit Dsui_0516 Dsui_0982
pccB propionyl-CoA carboxylase, beta subunit Dsui_0517 Dsui_0980
epi methylmalonyl-CoA epimerase Dsui_0512
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Dsui_0519 Dsui_1105
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Dsui_0519
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase Dsui_2205 Dsui_2347
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Dsui_2347
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase Dsui_1378 Dsui_0521
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Dsui_0437 Dsui_0105
lctP propionate permease
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Dsui_0519 Dsui_1105
mctP propionate permease
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Dsui_0516 Dsui_0389
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase Dsui_1637 Dsui_3369
prpB 2-methylisocitrate lyase Dsui_0011
prpC 2-methylcitrate synthase Dsui_2216
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
putP propionate transporter; proline:Na+ symporter
SLC5A8 sodium-coupled monocarboxylate transporter

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory